List parameters and their annotations in global section with -h option #976
Description
So suppose I have this workflow:
$ sos run workflows/fastqtl_to_mash.ipynb -h -v3
Available workflows
export
default
convert
Sections
convert_0: Generate utility functions
convert_1: Convert summary stats gzip format to HDF5
convert_2: Merge single study data to multivariate data
default_3: Extract data to fit MASH model
default_4: Compute for MASH EZ model and save to RDS
export: Export notebook to HTML file
it neatly lists all steps in the workflow. But under [global] I have something like this:
parameter: cwd = path('./gtex6_workflow_output')
parameter: data_list = path("data/eQTL_summary_files.txt")
parameter: gene_list = path()
parameter: msg = "GTEx eQTL summary statistics"
# maximum number of groups per HDF5 file
parameter: maxsize = 1000
parameter: cols = [8, 9, 7]
parameter: keep_ensg_version = 0
# number of null samples per gene to train MASH mixture
parameter: null_per_gene = 9
# a list of effect names (SNP names) to exclude from mash analysis
parameter: exclude_mash_effects_list = 'NULL'
# a list of condition names (tissue names) to include in mash output.
# Default includes all conditions.
parameter: include_mash_condition_list = 'NULL'
# size of MASH train set
parameter: mash_train_size = 20000
Correct me if I am wrong, but I thought we can list parameters with -v? I do not think it works, though. It would be great if we can list parameters along with what they are, eg:
--exclude_mash_effects_list: a list of effect names (SNP names) to exclude from mash analysis
Not sure if # is the best identifier for parameter comments to show, but we can also do ## or #' (roxygen convention). I'm just saying that showing parameter options could be useful when I make quick software-type of workflows for others to run without looking into the details.